Gitelman syndrome (GS) is an autosomal recessive, salt-losing renal tubulopathy caused by mutations in the SLC12A3 gene; however, it can also be acquired in patients with autoimmune disease, especially in those with Sjögren’s syndrome. Differentiating between the inherited and acquired forms of GS is clinically difficult. We report a case of inherited, not acquired, GS in a patient with Sjögren’s syndrome. A 41-year-old woman, who had been diagnosed with Sjögren’s syndrome at 27-years-old, had shown chronic hypokalemia (2.5–3.5 mmol/L). Laboratory tests showed hypokalemic alkalosis, hypomagnesemia, and hypocalciuria, corresponding to GS. Although acquired GS associated with Sjögren’s syndrome was initially suspected, a genetic test identified a novel homozygous mutation of c.1336-2A > T in the SLC12A3 gene, which resulted in aberrant splicing in the SLC12A3 transcript with the exclusion of exons 11 and 12. Thus, the GS was diagnosed as not the acquired but the inherited form. In the diagnosis of GS in patients with autoimmune disease, genetic testing of SLC12A3 is essential for differentiating the two forms.Electronic supplementary materialThe online version of this article (doi:10.1007/s13730-017-0271-4) contains supplementary material, which is available to authorized users.